Utilities               Utility functions for mzIDCollection object
attrExtract             Extract and properly format node attributes
attrExtractNameValuePair
                        Extract and format attributes from nodes with
                        name and value attributes
countChildren           Report the number of children with specific
                        name per node in an XML document
flatten                 Flatten an mzID related class into a table
getAdditionalPar        Extracts the additional, often software
                        specific parameters
getDatabaseFile         Retrive information on the database used in the
                        analysis
getDatabaseFilter       Looks for any database filters applied during
                        the peptide search
getDatabaseTranslation
                        Looks whether a translation table is present in
                        the mzIdentML file and reports it if found
getEnzymes              Extracts the enzymes used for digestion
                        specified as specified in the software analysis
getFragmentTolerance    Looks for presence of fragment tolerance
                        settings and reports these if found
getMassTable            Search for the presence of a mass table used
                        during the search
getModifications        Looks for presence of amino acid modification
                        settings and reports these if found
getParentTolerance      Looks for presence of parent tolerance settings
                        and reports these if found
getPath                 Get the correct namespace path depending on
                        version
getRawFile              Retrive information on the raw files used in
                        the analysis
getSearchType           Gets the search type as specified in the
                        mzIdentML file
getSoftware             Retrive information on the software used in the
                        analysis
getThreshold            Finds the psm threshold used in the file
getVersion              Get the mzIdentML version and check that the
                        version is supported
isRemote                Test whether a given string is a remote
                        resource
length                  Report the length of an mzIDpsm object
length,mzID-method      Report the length of an mzID object
length,mzIDCollection-method
                        Get the length of an mzIDCollection object
length,mzIDdatabase-method
                        Report the length of an mzIDdatabase object
length,mzIDevidence-method
                        Report the length of an mzIDevidence object
length,mzIDparameters-method
                        Report the length of an mzIDparameters object
length,mzIDpeptides-method
                        Report the length of an mzIDpeptides object
length,mzIDpsm-method   Report the length of an mzIDpsm object
mzID                    Parse an mzIdentML file
mzID-class              A class to contain data from mzIdentML-files
mzID-package            A parser for the mzIdentML file format
mzIDCollection          Create a new mzIDCollection
mzIDCollection-class    A class to handle a set of mzID objects
mzIDdatabase            A constructor for the mzIDdatabase class
mzIDdatabase-class      A class to store database information from an
                        mzIdentML file
mzIDevidence            A constructor for the mzIDevidence class
mzIDevidence-class      A class to store peptide evidence information
                        from an mzIdentML file
mzIDparameters          A constructor for the mzIDparameters class
mzIDpeptides            A constructor for the mzIDpeptides class
mzIDpeptides-class      A class to store peptide information from an
                        mzIdentML file
mzIDpsm                 A constructor for the mzIDpsm class
mzIDpsm-class           A class to store psm information from an
                        mzIdentML file
prepareXML              Parses an xml file and defines the namespace
show                    Show method for mzIDpsm objects
show,mzID-method        Show method for mzID objects
show,mzIDCollection-method
                        Show method for mzIDCollection objects
show,mzIDdatabase-method
                        Show method for mzIDdatabase objects
show,mzIDevidence-method
                        Show method for mzIDevidence objects
show,mzIDparameters-method
                        Show method for mzIDparameters objects
show,mzIDpeptides-method
                        Show method for mzIDpeptides objects
show,mzIDpsm-method     Show method for mzIDpsm objects
type.convert            An extension of type.convert() to handle XML
                        like logicals (lower case)
